yEd does not restrict the number of connections (or "edges") between two nodes. However, by default, edges start at the center of the start node and end in the center of the target node. Thus creating several straight-line edges between two nodes will result in all those edges lying above one another. There are several ways to "fix this problem":
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Run "Tools" -> "Route Parallel Edges".
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Do not create straight-line edges only but add bends to your edges. You can do so by releasing the mouse on empty space after starting an edge or by dragging an edge after creation.
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Use different start and/or endpoints. If you press and hold SHIFT when creating an edge, the edge will start/end at the mouse position instead of the node center. Alternatively, you may select an existing edge and adjust its "Source Port X", "Source Port Y", "Target Port X", and "Target Port X" properties.
